Image: Eric Erbe (via Wikimedia), digital colorization by Christopher Pooley, both of USDA, ARS, EMU. Electron micrograph of a cluster of E. coli, a member of the microbiomes of humans, dogs, and other species.

“Wasp’s Got Guts” in the September print edition of Discover Magazine discusses how wasp microbiomes set them apart. Turns out, our guts can be pretty different from one another too.

Rob Knight, a microbiologist at the University of Colorado, Boulder, and his colleagues want poop from every person in America. And over the past couple of years, thousands of citizen scientists have complied by shipping little vials of feces to his lab. To clarify, it’s not exactly the poop that these scientists are after but the hidden germs within. Knight and his colleagues study the human microbiome, the mosaic of microscopic organisms teeming on and within our bodies.

In recent years, research on this host of microorganisms is revealing that our microbiome is as intricately linked to our health and bodies as any native human tissue. The human body is, in some sense, a scaffold for a vastly greater mass of microbes – by some estimates, making us 90% microbial. In turn, our microbes provide for us by playing “important roles in metabolizing components of our diet and drugs,” says Knight. “Disruptions of the gut microbiome have been linked to a wide range of diseases,” where the disappearance of certain key organisms or changes in the species represented in the gut goes hand in hand with illnesses like obesity, diabetes, heart disease, or neurological diseases. In other words, the kinds of bacteria living inside you figure into how healthy you might be.

But learning exactly what a healthy or unhealthy microbiome looks like is “the holy grail,” says microbiome scientist Jeff Leach. “The problem is there’s so many variables.” Differences in diet, genetics, and environment can change the composition of your microbiome. Adding to the muddle is the fact that nigh all the best studies on the microbiome are done on mice, and transferring findings from animal models to human beings is notoriously difficult. One of the first steps to solving these problems, Leach says, is to start comparing the gut microbes of people with different diseases and lifestyles.

The Human Microbiome Project, a National Institutes of Health funded initiative, had begun doing something similar in 2008 – but it only looked at the microbiomes of 200 people. Leach is dreaming much bigger. With the help of Knight and one of their colleagues, microbiologist Jack Gilbert at the University of Chicago, Leach started attempting “to sequence 20 thousand, ultimately maybe 100 thousand individuals to get large scale patterns not only across America, but the planet as well” through a citizen science project he was calling the American Gut.

“We launched it over Thanksgiving of 2012, in part because it’s a time of year when many people are thinking about their gut,” says Knight. Two IndieGoGo and one Fundrazr campaign later, over six thousand people have sent swabs of their microbes to the American Gut researchers. If you get sequenced, American Gut will send your results back to you, letting you know what’s in your gut, on your skin, or (if you want) in your dog.

One of the main goals of the American Gut was to begin putting small scale clinical experiments into a wider context, says Gilbert. “If I do a clinical study of a hundred autism patients,” Gilbert says. “And if I see in 3 autism patients, there are three bugs that are really enriched or four bugs absent compared to [people without autism]… I want to know how well distributed those three or four bugs are in a wider population.” With a database of thousands of people and counting, Gilbert and the labs of 36 other principal investigators involved in the American Gut project can begin analyzing these types of comparisons and better understand some of the broad health implications of our microbiome with more statistical integrity.

“I think it’s a very promising resource. It will be a source to do a lot of in situ studies,” says Maria Dominguez-Bello, a microbiologist at New York University. “The data are there if you want to study Type I or II diabetes or all sorts of things.” The American Gut project is focusing on autism patients right now, the results of which should be coming out in the next few years, but already the data are uncovering some interesting trends.

For instance, Dominguez-Bello and Leach’s research is finding that different ethnic groups and cultures have very different microbiomes from those in the American Gut. And a recent analysis of the American Gut dataset is revealing that lifestyle changes in diet, sleep, and exercise are altering the composition of our microbiomes. “We see in the American Gut data that people who consume more alcohol have a greater diversity of bacteria than people who don’t,” Leach says. Since diversity is thought to be protective, “hopefully that doesn’t tell people to drink more, but who cares.”

That’s not to say you should start fussing over what you do or don’t eat based on the microbial consequences. We’re still a far cry away from being able to sample someone’s bacteria and curate their gut into an ideal microbiome, and we’re a long way off from fully understanding how the denizens of our microbiome interact with our bodies. But Leach and Knight believe the American Gut project is helping to move the research in that direction. At the same time, the project is a way for them to give back to the community supporting this research.

“We wanted to use [American Gut] as a teaching tool for the general public. When you have 20 thousand people empowered with the information on the composition of their microbiome,” Leach says. “It’s an opportunity to teach people or get people more actively involved in their microbiome.”

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gseattle

*Great* idea. I took part in that (and another one like it) and have not found the results so far very illuminating, 3-d colored venish diagrams and big names in the bacterial kingdoms that mean little (pun acknowledged). Can’t wait for the next gen and/or competition.

http://blogs.discovermagazine.com Longmire

Researchers in this field should definitely take into consideration racial stereotypes which would certainly help them break down the data to a more digestible level.

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About Angus Chen

Angus Chen is the managing editor for the SciStarter Blog network which includes the Discover magazine "Citizen Science Salon" blog and the Public Library of Science's Cit Sci blog. And he's a freelance reporter and producer at WNYC Public Radio on "The Takeaway," where he covers general assignment news. You can also read his work with Science magazine. He was once a scientist studying geology and ecology, but now spends his days typing and scribbling and sketching furiously.